Thank you for referencing that link. That was something I read a while back and could not remember where I found it. It has lots of good information and a nice read especially for AR-newbies.
The military has a set of specifications (the often mis-used term "mil-spec") which is a minimum set of specifications that they want. Whichever company meets those specs and has the lowest bid gets the contract. They also look at whether or not the company can meet the production schedules and other things as well. The miltary gets M16s/M4s from Colt, FN and I believe Sabre recently got a contract as well. I think that Bushmaster also got a military contract to provide M16s for some foreign countries. None of this means that these are "the best", only that they meet the specs/cost that the government wants. Some commerical AR manufactures do not meet mil-spec and others exceed them. Which one would be best for YOU would depend on what YOU want to use it for and how much YOU are willing to pay. The often seen chart by rob_s (http://spreadsheets.google.com/pub?key=pwswheghNQsEuEhjFwPrgTA&single=true&gid=5&output=html) does show a lot about which manufacturers meet which specs, but again, that does not mean it shows what is the best for YOUR circumstances.